23d2f6c84c64c7569e6e621ddcad8316 *DESCRIPTION
dda676dcad4e834b6ccd1333d99e1f72 *NAMESPACE
1ebec02dfe9feb8e861d3d469154ea19 *NEWS.md
1bd3fe342c314678b16e70f4b926f1e5 *R/add_columns.R
c3f30eba2911d00f4c89427dde2c469c *R/add_rowcol_names.R
ac9020c25e3ee9dc2cd1d58b1317ffc3 *R/add_synonyms.R
f573d8df16f19416ef3256ed6839d329 *R/aggregate_mapped_genes.R
7b675c6291c689975fffd82439589128 *R/aggregate_rows.R
3684681a227de0e4d685d9cf97b7cad5 *R/aggregate_rows_benchmark.R
1b363cac4587d15819616eac1db180a4 *R/aggregate_rows_monocle3.R
20e1daa3764a6774ebed70b6b5dd9959 *R/aggregate_rows_stats.R
04adcfb17f35b94eab4abe033449a7c3 *R/all_genes.R
4c98f89a1fe6c20c32d657a80c03909d *R/all_genes_babelgene.R
4a4ce8786f259102087fae71093a87ee *R/all_genes_gprofiler.R
5d438f20793a2a16df5b14622db10fba *R/all_genes_homologene.R
78daaf3273ef27fd8013bff1a093d323 *R/all_ranges.R
a73c659db99422edcf376625e9d56429 *R/all_species.R
dc2948fdd08cbd5eee09488477e351cb *R/as_delayed_array.R
3214a9ce601f641e82cc09d6520b2ae6 *R/as_dict.R
7fbe6d5d2da953e89f87f79d08cbdfa5 *R/as_table.R
e5db9284a09782144400887977c53740 *R/check_agg_args.R
35f9e7a086503f3d142913c267a0f9e4 *R/check_agg_opts.R
a17149085a6281f669c774cfee5e5194 *R/check_bool_args.R
901f44f1d4d83c62a9a97430629cd589 *R/check_gene_df_type.R
29e40f4489c15d28dc571d8cc7a91095 *R/check_gene_map.R
2915d9c2be6584a4b68848bf62fa5eb9 *R/check_gene_output.R
b104cf54901405c4f37061b11c7b42a1 *R/check_keep_popular.R
9c55211cfc759f82d605795486404497 *R/check_matrix.R
0835b935685857badff2d1a7bdc2082b *R/check_rownames_args.R
59142ba90a97afb5f3d92cb3fe32386b *R/check_sparseMatrix.R
5642785523827a403f6146e5bfa003fb *R/check_species_babelgene.R
000e1c0fe34884741830ce536c29bde5 *R/common_species_names_dict.R
0f30d97924bd802b6479e0478d69acae *R/convert_orthologs.R
e48587560bd14a373c06e62104705466 *R/create_background.R
7ecefe42f3e44b4982e58f80cffbc1a3 *R/dMcast.R
d93865f76eeda3eb0a37d066b091b572 *R/data.R
7a74c4e37362814f073800d2f25598da *R/drop_non121.R
17565f0f8e60e047c23d89a8a04ee973 *R/drop_nonorth_genes.R
395ba945d2205bf6fd243a0b1e189fa5 *R/earthworm2human_map.R
5cf5bbdeb14ec384228edd338feaef70 *R/extract_gene_list.R
a9e56d3ca9001073621364b379402f79 *R/filter_gene_df.R
bf76b3a4fa93708957741b60820d3b03 *R/find_all_nas.R
28aeae662cad5a6d17e386050257c9c6 *R/format_gene_df.R
b5ff1bac7f9990b749f54baecae78424 *R/format_species.R
1765ffb07c6acd424896856632e62452 *R/gconvert_target_opts.R
9e793a69e8037383985a97abe4d83bfd *R/gene_input_opts.R
93d4bf186786c365c0c3e2791e1b1175 *R/gene_output_opts.R
41adfcef2f9166671af5fde9bc0c9cce *R/get_all_orgs.R
34297b51f159015a45c77401384dd084 *R/get_data_check.R
d180ffd56696466efb340880bc6edbb2 *R/get_orgdb_genomeinfodbdata.R
2b89472b4414c7c48bb65aa354fbceda *R/get_orgdb_gprofiler.R
a47f0966464d393f970f7bc193ebf59d *R/get_silhouettes.R
89f41b5019176943518f70e6053d4174 *R/ggtree_plot.R
f863d09673637c0ba0ef5b8eb8fa8adc *R/infer_species.R
a61d6ad4587988a02760824faf4565e1 *R/infer_species_plot.R
3f5a608e574fe258214fbff24022d6a9 *R/invert_dictionary.R
cf1aac8d9d80d24edf956e3bbd115182 *R/is_converted.R
52bd2101acf3566da92f16327a3a611a *R/is_delayed_array.R
e8aebcdec830deea9e9943a2f5ed399d *R/is_human.R
e739b18dbc743301544735a9d858e141 *R/is_matrix.R
446ee264a7c02b34de7fd4a74003a7ab *R/is_sparse_matrix.R
30c542249ea3a5cda3f13a91b00d0558 *R/load_data.R
002193fdf0b66259925076ef0dcd9680 *R/load_rda.R
3ceff8d6d2a7ef4ad0761a1ddda1d1d4 *R/load_rds.R
69b8af5025a798603c98c0883868f93f *R/many2many_rows.R
adce69cbb225d2cd28a182a76058bf67 *R/map_genes.R
e2f8a8bac5119d5a9b1b65c487501b5d *R/map_genes_planosphere.R
cc1108f484383603aa356a2885dcc04c *R/map_orthologs.R
efee65dac70248bbc9cfdfc16c26d38f *R/map_orthologs_babelgene.R
9b4b10762de735506b72eea2f0517e72 *R/map_orthologs_custom.R
d0e4391428de447ba76e9796a975ad03 *R/map_orthologs_gprofiler.R
22588cb3b5f936606d91d179fba27bba *R/map_orthologs_homologene.R
36f367733df70e318a0027fa2defecc8 *R/map_species.R
8824651361f00db1c19224a0f8892fa7 *R/map_species_check_args.R
ac75b980f420c95eee3c0171dc481516 *R/message_parallel.R
31afbec23322d7cf6b584c83772b641f *R/messager.R
6f1753d94584f463fb468a72b1dbbcde *R/method_fill_colors.R
4ccfa07831a4323b982e9f8572cd2e38 *R/methods_opts.R
2a081083994dd48889332718d49d007d *R/non121_strategy_opts.R
ecfae884931a38d43ee4f545f83202e2 *R/package.R
1c056aa02466984b60190c87a5de77b0 *R/plot_benchmark_bar.R
027153322b05343ff4e0343ef3e7a835 *R/plot_benchmark_scatter.R
05e546e7cb5a13222a3a96196941dbfe *R/plot_orthotree.R
39e371a24aaaa5a7bb3c5c9530d3d657 *R/plot_orthotree_metadata.R
6da8e239b2134e6f300ca17c0350eb30 *R/prepare_clades.R
f6fa2c8117179167dadbd07779f05587 *R/prepare_tree.R
6186f7792e7325d906bf038e42577ec8 *R/remove_all_nas.R
20c4bac904bd696f22653eb4e299a7b5 *R/remove_image_bg.R
c12cc1c80eb5e98258d2575a3733a745 *R/report_gene_map.R
203eed593808a3977e70e65d54488814 *R/report_orthologs.R
8d6063d1fdd82fe6fa39ada5b41565ba *R/report_orthologs_i.R
a2dc10112e3ac9dc3a85285c59e7562c *R/rotate_clades.R
86179def59b49321274b6e77bad0feb6 *R/run_benchmark.R
67f30f90de56207c2842a4ab99fcef49 *R/run_benchmark_once.R
c97d1f61f73b0933c466237e455382f9 *R/set_gprofiler.R
251faf7bc9f7c7a736664a0d4e1cb17f *R/sort_rows_func.R
abec2bea7c3747d190db2f835abf103b *R/sparsity.R
9155a9a65f78f3868d4fda26d6a811e0 *R/sysdata.rda
cbbb884f51acdf4cbb2ff3acb43344cb *R/taxa_id_dict.R
c9cee37d4c20f13803498cde47465bbb *R/to_sparse.R
d964f1a6999ebba801caff934336f989 *R/use_cache.R
44beaa76f57d42ecfc2ed7ccee1d6858 *README.md
db4aea3650b9f63156b513c9090c87b9 *build/vignette.rds
07193cd179e88787b4e037aa73343871 *data/exp_mouse.rda
781d1d656e89f810b0f6b7fc982efcbb *data/exp_mouse_enst.rda
75dec8981674cecd06044a37b4b1e552 *inst/CITATION
c375ed52bb1d00829acc84aef2f5ce54 *inst/benchmark/bench_res_example.csv
7f69a52767ecf9a1b1cf5c3bc2852843 *inst/benchmark/benchmarks.Rmd
eed8c59228a15b679f1c84a7363851ab *inst/benchmark/benchmarks.html
039067f20529536be39479e43d874975 *inst/doc/docker.R
ff48d0a4bd4822a60ee8ecb27ce6ce5c *inst/doc/docker.Rmd
2cd72f85e25b9cd40c3390920ede622c *inst/doc/docker.html
59fe8b10c2f01c03f28479669cae964c *inst/doc/infer_species.R
d2b38a5b2b35bd73d3fc27dc6ee2f120 *inst/doc/infer_species.Rmd
3c26556c9cf988ad5ec9d57dbf138c4a *inst/doc/infer_species.html
25b5b420deefa8cddc187161aa09e74d *inst/doc/orthogene.R
f97788f0e8e359c9e81143e8d1fa8260 *inst/doc/orthogene.Rmd
c3fcc122f9ac88c7190248747b880c0a *inst/doc/orthogene.html
cee814272a6c05d80d784fbb151b866d *inst/extdata/gprofiler_namespace.csv.gz
c5171837647f94998c67ac3ff96bb35c *inst/hex/hex.png
c562f2ff4988a39d2279bacd1c614d66 *inst/hex/hexSticker.Rmd
2f9f541b7a07d51be15d8b3811fb2d7d *inst/hex/hex_nowhite.png
b3e00d264cca2d9c02f39e8671189d8d *inst/hex/purple_blue.jpeg
9b327af4f72efdb42dbf77467b2acc6a *inst/orthogene_1.15.02.pdf
7fc6bbf317058b93181056fbd4d4951c *man/add_synonyms.Rd
0273ea7874b169974caedb6ccb9338fe *man/aggregate_mapped_genes.Rd
ead0ec4a0b05c928a8d78e73cb3071dc *man/aggregate_rows.Rd
d31ac9c3e49f3c9aeefe2b73b928e400 *man/aggregate_rows_monocle3.Rd
c491c375f104ef38421bf7ac7f82544d *man/all_genes.Rd
0c16847905691291f7915ae11a4b1e58 *man/all_genes_babelgene.Rd
09a052954553730ec59d7bb874644146 *man/all_species.Rd
c340ef3df2100e1dcf3698cb38e0c5ba *man/check_bool_args.Rd
e99a2742501d22a1753d81a4c956bc5c *man/check_gene_df_type.Rd
65d05c5dfb6a360a1271e9f763db0a14 *man/convert_orthologs.Rd
2d52d7c4fd29ce153d01dbb46f0cc019 *man/create_background.Rd
e3614308e5c1b171fc013288f950a8eb *man/dMcast.Rd
173898c6bf6381d98dc172ac3afdcab2 *man/earthworm2human_map.Rd
10ab7e2b329a2d94d605bad6b74a41f3 *man/exp_mouse.Rd
2a205c9d498b35c6a5ceb32044cd5ad7 *man/exp_mouse_enst.Rd
d1db4f8ff2688c1789d71c64a266b6a6 *man/format_species.Rd
f53a020ed531c3dd43409b51372f0538 *man/get_orgdb_genomeinfodbdata.Rd
c050ebb02674241b7d0eccef03d7f3d9 *man/get_silhouettes.Rd
c7ab2c4f9878cefbfe84b7d4f37974df *man/ggtree_plot.Rd
6f40f7b24ccb262b9a3e8a6df01e44a0 *man/gprofiler_namespace.Rd
32e345bb124b0b0c297f4f24ef0e10dd *man/gprofiler_orgs.Rd
39d1326713c22b3b6dcd3bfc495b1d79 *man/infer_species.Rd
701cde7edb7424fc5359aedb437fcf71 *man/infer_species_plot.Rd
9c559d63a5151797993577e80502b19f *man/invert_dictionary.Rd
a81c3f1c941627a1e64c6ba2a5cb5db2 *man/many2many_rows.Rd
1353fe21c5d7c7c6036a7ecadeb262a5 *man/map_genes.Rd
3150c28cfa0a47e2f497f3c487684254 *man/map_genes_planosphere.Rd
c6b3f2950a2c54dc790934f4bb2f600c *man/map_orthologs.Rd
8ff2c1559ad23201196c96cc8fadbf58 *man/map_orthologs_babelgene.Rd
8bf6ab6362020f8de5ad92fad874e076 *man/map_orthologs_custom.Rd
5c79c536b6381fd0cf0c6c0bf23a4674 *man/map_orthologs_gprofiler.Rd
ce146e7348dc5294446195b2f3cf3664 *man/map_orthologs_homologene.Rd
9a3d5342d40ee907cfcc178635ce63cf *man/map_species.Rd
1cd9e63d25b4ed449b6602d5c061f3e4 *man/message_parallel.Rd
c387b83d9e9064e8c1dd2472762939a1 *man/orthogene-package.Rd
32caf65d07f670a0a937cf4a5e34f0a0 *man/plot_benchmark_bar.Rd
db6eeb8eb1abdd9b6b3efb904b89da61 *man/plot_benchmark_scatter.Rd
8648ce7034a2be0b33a15b204ade8bc9 *man/plot_orthotree.Rd
5e5e6e3081b1b9331c2e1b7e832bfcb6 *man/prepare_tree.Rd
247c8e31299dbca2baf3cdd3532f0c54 *man/remove_image_bg.Rd
a1b98ae272107fcc68aeefc784fff0ce *man/report_orthologs.Rd
c80ba7252f2a9a69d4e10d3cce9f6c19 *man/run_benchmark.Rd
87a7c29cd8bc286a6b6086612a4855f0 *man/set_gprofiler.Rd
d85d4e5e6c0071869fd569572a693f6d *man/taxa_id_dict.Rd
bdb53e4cccf93ad583ff9b93251d6ea1 *tests/testthat.R
d9967b48a9f25045cfc9adf31057de09 *tests/testthat/Rplots.pdf
aced95b6b471b1a2aa997504bd92eaf7 *tests/testthat/test-aggregate_mapped_genes.R
e325a6683a159bd1a4549ce5c0de1aff *tests/testthat/test-all_genes.R
bb9c9cf85d39b8991fab1bf1592eb52c *tests/testthat/test-all_genes_babelgene.R
50b70dad3b299e172637e9131fab78a4 *tests/testthat/test-all_genes_gprofiler.R
0750234f1249e70cf4f752a6ba07317b *tests/testthat/test-all_species.R
2eece204ec303014fdff10acce44a1a2 *tests/testthat/test-check_rownames_args.R
70f783a7a98741532c84d4bf72a63c80 *tests/testthat/test-convert_orthologs.R
802ed103d2d9e60322b01aeae044bb4d *tests/testthat/test-create_background.R
cc879466938283326eb8164e489b87a7 *tests/testthat/test-earthworm2human_map.R
d9b267f61800285634563059e69d10af *tests/testthat/test-infer_species.R
2bc612943031bd4b4b24843bbb254573 *tests/testthat/test-invert_dictionary.R
7d51633248f7986b5711af4466ff34a5 *tests/testthat/test-load_data.R
0215dd0027b373985574ca4a3d89aa29 *tests/testthat/test-map_genes.R
4e3a09db3c8c2b6b75aae62c99dbb87e *tests/testthat/test-map_orthologs_babelgene.R
8e6bd3dbd446fcec08154d78ebd575d5 *tests/testthat/test-map_species.R
7f3a3ac293c95530dd1975f2cc3c3379 *tests/testthat/test-plot_benchmark_bar.R
a06a85cefa2d440a8e0b4d80be2870c0 *tests/testthat/test-plot_benchmark_scatter.R
68a69f30279742fdcb6bcb34c5f89ac2 *tests/testthat/test-plot_orthotree.R
2884a59b10e21aa968deef28106ebc38 *tests/testthat/test-prepare_tree.R
560dc88394d053a939fc57f1aadeb262 *tests/testthat/test-report_orthologs.R
af2d57c29f78f7a58654a8ef5ce3d6cd *tests/testthat/test-run_benchmark.R
b2e24a3c60e3cb6a3ebd0a9e3753cf73 *tests/testthat/test-sparsity.R
ed6c81192cd54bf044fa523bb3b1aa09 *tests/testthat/test-taxa_id_dict.R
ff48d0a4bd4822a60ee8ecb27ce6ce5c *vignettes/docker.Rmd
d2b38a5b2b35bd73d3fc27dc6ee2f120 *vignettes/infer_species.Rmd
f97788f0e8e359c9e81143e8d1fa8260 *vignettes/orthogene.Rmd
